I initially tried to bootstrap on a case-insensitive filesystem, with
the insensitivity flag, but that failed, with a "mkdep: gcc -isystem
/usr/include: not found" message, on linking libncompat. I then tried
again, on a case-sensitive HFS+ disk image, and got the same behavior.
The pkgsrc tree was checked out today. I have the disk image mounted
on /Volumes/pkg, and /usr/pkgsrc -> /Volumes/pkg/pkgsrc and /usr/pkg
-> /Volumes/pkg/pkg.

I just ran into this as well, on 10.4.11 (PPC) on a case-sensitive
file system (case-sensitive HFS+).
Something changed between my successful bootstrap on or about
200804070100Z and this message.
(I wiped my initial bootstrap and packages, updated pkgsrc, and was
trying to bootstrap anew.
--
John D. Baker, KN5UKS NetBSD Darwin/MacOS X
jdbaker(at)mylinuxisp(dot)com OpenBSD FreeBSD
BSD -- It just sits there and _works_!
GPG fingerprint: D703 4A7E 479F 63F8 D3F4 BD99 9572 8F23 E4AD 1645